General tracing parameters - ekatrukha/BigTrace GitHub Wiki

Settings in this tab define parameters for Semi auto tracing, One-click tracing and Full auto tracing modes.
It appears in their corresponding settings windows.

Curve thickness along axes parameters specify the approximate thickness of curves of interest in each dimension (in pixels!).
A good estimate for these values can be made by plotting the intensity profile perpendicular to a curve in each dimension and fitting it with the Gaussian function. SD of this Gaussian is the value that is needed.

Alternatively, one can look at the rendered TraceBox volume, if the curves are too dotty, these values can be increased.

Since its value is in pixels, you need to take into account voxel anisotropy (the difference between pixel width/height and depth).
For example, if your curve looks like it has the same diameter in X,Y and Z, but the voxel depth is 3 times larger than voxel width/height, then the curve thickness in Z should be 3 times smaller than X and Y.

In practice, it is an SD of Gaussian Derivative convolution filters for each dimension used to calculate the Hessian matrix.

Set ROI diameter X.X times MAX/AVG/MIN of all SDs overrides ROI thickness specified in the current active Groups selection for the mentioned above tracing modes and sets it to the selected values.

Trace only clipped volume checkbox decides, in case of the clip applied to a dataset, whether the tracing will continue outside the clipped volume.